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The tests described in Methods revealed a number of differences between the three mapping applications.
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By looking at the transitions between the three maps, an overall increase in Gini coefficients is expected.
After their removal the remaining corresponding markers are in close agreement between the three maps but still reveal inconsistencies with the sequence assembly.
Based on the number of shared and specific recombination coldspots and hotspots (Venn diagram in Additional file 10), we calculated a Jaccard index to assess the similarity between the three maps (three pair-wise comparisons).
Between the two mapping methods, all QTLs were different except for qSIS11.2.
Unless Apple wants to take on the competition authorities, it will have to approve the app, and let users choose between the two mapping systems.
Of these, 110 were shared between the two mapping approaches.
One exception to the generally good agreement between the two mapping methods is isolate PG311-1.6.
Among the tested primers, 195 were polymorphic between the two mapping parents.
Among the 816 effective SSR primer pairs, 195 (23.9%) were polymorphic between the two mapping parents.
In addition, 40 (49%) and 50 (61%) of the 82 eSNPs segregated between the two mapping parents for AMF2 and MMF2, respectively.
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